25 Feb 2015

In recent years, the trillions of bacteria living in
our guts have risen from obscurity to stardom. Hyped press releases claim that probiotics and faecal transplants might one day treat almost everything, from bowel inflictions to obesity. These studies often involve mice, but are these rodents really a suitable model for microbiome research?

The gut microbiome has been associated with an
ever-growing list of diseases, including obesity, diabetes and even mental
disorders such as anxiety and autism. Much like the Human Genome Project around
15 years ago, the booming microbiome research field has promised to deliver new
revolutionary treatments, some as simple as eating a yogurt. Perhaps inevitably
though, history repeats itself. After a few years of frantic microbiome sequencing and many new biotech start-ups,
microbiome researchers are now having to face the hard questions: are the
changes in the gut microbiome associated with certain diseases a cause, or a
consequence, of the disease? How on earth can bacteria in the gut affect other
parts of the body, such as the brain? What are the molecular mechanisms behind all
this?

E. coli bacteria thrive in the gut.

Studies in humans can at most reveal correlations
between the microbiome composition and a given disease. For example: Bob is obese
and happens to have a microbiome with lots of bacteria X, but John, who is
slim, doesn’t. This suggests that bacteria X cause obesity, yet, there’s also a
good chance that in fact it’s the other way round: obesity might somehow
promote growth of bacteria X. Or maybe this type of bacteria thrives on Bob’s
diet, or it simply prefers the unique environment of his gut.

It is virtually impossible, and unethical, to perform
experiments in humans to explore causal hypotheses (does bacteria X cause
obesity?) and control for confounding factors like diet and genetic background.
Microbiome researchers have to use the next best thing: mice. There are,
however, growing concerns within the scientific community that more often than
not, data from mouse can’t be extrapolated to humans for clinical purposes. Or
at least, not easily.

In a new study, Jeroen Raes and colleagues at the KULeuven
University, in Belgium, carefully compared the human and mouse gut microbiomes to
assess the strengths and pitfalls of this model system for studying microbiome-related
diseases.

“Microbiome research, notably its association to
inflammatory diseases, relies heavily on mouse models […]. It is essential to
know the qualities and limitations of each model to choose the correct one to
test specific hypotheses”, says Sara Vieira-Silva, one of the authors conducting
the study.

Can mice recapitulate the human gut microbiome?

Mice are great for biomedical research. They share most
of our genes, and have similar anatomy and physiology. With the many available
genetic tools, scientists can easily and quickly discover the function of
literally any gene in the mouse genome, and recapitulate human disease in a
controlled experimental set up. So where’s the catch? The problem is that although
mice and humans share many similarities, there are also many differences.

Rae’s
team performed comprehensive statistical analyses for all gut
microbiomes from mice and humans published to date. These new data tell us what
types of bacteria live in the gut in various scenarios (disease, diet, genetic
background…), as well as their relative abundance. The team first compared the
gut microbiomes of healthy humans and mice. And the differences start here.

Human and mouse guts
have predominantly two ‘families’ of bacteria—Bacteroidetes and Firmicutes—but
within these groups, 85% of bacteria species found in mice are not present in
humans. And the bacteria found in both? It appears their abundance in the gut
also varies between mice and humans; when you’ve got a lot of a certain
bacteria in mouse, you may find very little of it in humans, and vice versa.
The authors stress that many of these differences could simply be a result of
technical limitations, like methodology or interference from external factors
(diet, age, etc).

Mouse models of disease

There are over 60 mouse models of Inflammatory Bowel
Disease (IBD), but none fully recapitulates the disease. Even so, the changes
in the gut microbiome of patients with IBD (when compared to healthy people)
are similar to those observed in IBD mouse models. For example, there is a significant
reduction in bacterial diversity in both IBD patients and IBD mouse models. However,
some specific bacteria species will be more (or less) abundant in mouse but not
in IBD patients. The same goes for obesity models. Overall, mice fed on
high-fat diet, and also leptin-deficient mice, which cannot control their appetite,
recapitulate the microbiome changes observed in obese people. But there are
many discrepancies in the data, again likely due to external factors that are
difficult to control, at least in human studies.

The conclusion? Well, mice are not people. Raes and
colleagues warn microbiome researchers that extreme care should be taken when
trying to extrapolate findings in mouse to humans. They should also make bigger
efforts to standardise their protocols for animal handling and data analysis, and
to share mouse models to eliminate any genetic variability that might skew the
data.

“Most limitations of murine [mouse] models for
fundamental microbiome research can be overcome by methodical study design and
statistical testing: either eliminating or keeping track of possible
confounders (e.g. diet variation, genetic background) and testing for their
influence on the results”, says Vieira-Silva.

Nevertheless, the authors conclude, when it comes to
understanding the causes and molecular mechanisms behind human disease, mouse
models seem to fit the bill. “Although the mouse microbiota composition is not
identical to the human's, most mechanisms of microbiota-host interaction will
be shared between mice and humans” concludes Vieira-Silva. “Mice models allow
us to study these mechanisms with direct controlled experiments, towards the
ultimate aim of providing therapeutic solutions.”

5 Feb 2015

Now happily living on land, our Devonian ancestors tried many ways to get out of the murky waters. Jenny Clack has been studying the water-to-land transition of vertebrates for many decades. Her discoveries broke dogmas and rewrote textbooks.

Jenny Clack's passion for palaeontology began at a young age, but unlike most children, Clack
found dinosaurs “rather boring” and was instead fascinated with weird older
creatures from the Devonian era, over 360 million years ago. After completing an
undergraduate degree in vertebrate palaeontology, Clack worked for about seven
years as a display technician at the Birmingham
City Museum, until she finally had the opportunity to do a PhD with Alec Panchen at
the University of Newcastle upon Tyne (UK). Clack’s talent quickly got noticed,
and during her PhD she was offered a position as an assistant curator at the
Museum of Zoology of the University of Cambridge (UK). At Cambridge, Clack had
an insight that would transform her career and her life. During an arduous field trip to Greenland in 1987, she found spectacular remains of Acanthostega, a tetrapode (four-legged vertebrate) that would overturn decades-old theories. Clack was the first woman in her field to
become a fellow of the Royal Society, won numerous distinguished awards and is
currently a professor and curator of vertebrate palaeontology at the Museum of Zoology of the University of Cambridge.

When did you know you wanted to be a palaeontologist?

Clack: I was always interested in natural
history generally, and as quite a young child, from the age of seven or so, I
collected plants and fossils. And certainly by the age of ten I was interested in palaeontology and
rocks, and I used to borrow books from the library. I would read geology books
and books on fossils and natural history instead of what my teachers would want
me to do, which was to read novels, of course. Throughout school, I was
always interested in natural history and decided that I wanted to do zoology
degree, and went to the University of Newcastle upon Tyne. One of the reasons
for choosing Newcastle was because it had a programme in palaeontology as
part of the zoology degree. It was just the idea of these ancient creatures... I was always interested in the earliest stuff, rather than dinosaurs. I had
a series of volumes of a children encyclopaedia that had sections on various
periods from the Palaeozoic, and they were really my inspiration. I wanted to
know about the very old fishes and early animals, like the amphibians that were
described in those days. When I got the opportunity to study at university then
obviously I decided that’s where I wanted to go. But it wasn’t straightforward
by any means.

What was it like for
a little girl back in the 1960s to pursue an academic career?

Clack: It was more that the teachers
obviously knew that I was interested in that kind of thing. I remember one
of the teachers in junior school identifying me as an “academic type”, even
though I had no idea what that meant at the time. Certainly, my parents always
encouraged me to do whatever it was I wanted to do. They took me on holidays to
places where I mind find fossils and other elements of natural history. […] My
career has been a bit of a complicated path because I didn’t go into
palaeontology professionally after my degree. I did a Museums Study course, and
then worked seven years in the City Museum in Birmingham. And it was only when
I had the opportunity to do a PhD that my career really started.

How did you eventually get into academia?

Clack: It was partly encouraged by the
museum itself because they allowed people to do three weeks of private studies
per year and my mentor-boss at the time was very supportive of this. So, I got
back in touch with my old mentor, Alec Panchen, in Newcastle and asked him
whether he had any projects I could work on, and in fact he did. He
directed me to a specimen in a museum in Bradford that was a Carboniferous
tetrapode. To cut the long story short, I took that specimen to his lab and
worked on it for the three weeks, during which time I found that there was
quite a lot more to the specimen than anybody had realised. And then Panchen
said I could probably get a PhD from that material; he applied for grants and
got it.

Was it at this time that you decided to focus your career on the
fish-to-tetrapode transition?

Clack: I was interested in the
same sort of field that Panchen was, which was Carboniferous tetrapodes, so it
was a natural expectation that I would study something of that nature. And
indeed, the PhD started that ball rolling. While I was still doing my
PhD, I applied for a job as an assistant curator at the Museum of Zoology of
the University of Cambridge and much to my surprise they offered it to me. This
would not happen today. There is no way someone who hasn’t finished their PhD,
has got no published papers and has no reputation would get that kind of job. Now, you would have to have a postdoc, at least. I had the museum qualifications and
the research background that they were interested in. I fit the bill I guess
[laughs]. And it wasn’t until some years later that the opportunity to look at
the Devonian material came about. After
I had finished my PhD in 1984, I wondered what on earth am I going to do next?
I didn’t have any very clear ideas. My colleague Andrew Miller said something
will come up and indeed it did! It turned up in a drawer in the Earth Science
Department across the road. This was a drawer full of Devonian material from Greenland
that a former student there had collected without realising what it was, or its
potential importance. And from there we got the expedition to go to Greenland
in 1987 and collected more of this material, which turned out to be extremely
important. A very lucky break indeed.

Fossil remains of Acanthostega.

What exactly did we learn about the water-to-land transition from
your discoveries of Acanthostega?

Clack: There were two major discoveries.
The first one was about the story we had been told that, as
soon as these creatures came onto land, they developed the capacity to hear
air-born sound. And it became clear from the work I had done in my PhD, and the
work on Acanthostega, that
this couldn’t possibly be the case. The story of the
origin of terrestrial hearing became much more complicated and it was
corroborated by people from other palaeontology groups. But probably the most
widely known discovery was that Acanthostega had eight digits in each limb. That was a real
surprise. It took a little while for people to believe that this was the
case because the dogma was that there were five digits in primitive tetrapods.
And here we had an animal with eight digits on each limb! We then discovered
that a Devonian tetrapod that had been known for decades called Icthyostega had in fact seven digits on
its hind limb, and this complemented what we had known about a Russian animal
from the Devonian, which has got six digits. All of a sudden it became a
pattern of multiple digits in the earliest tetrapods with limbs. This changed
the idea of how limbs evolved and what they evolved for. If you look at the old
books from the 1940s, for instance, you get an idea of what they thought a
proto-tetrapode looked like, and basically it looked like a fish that has got
legs with five digits on, and it’s making forays onto the land. But actually
our work suggests that the animals already had limbs with digits before they
ever came out of the water. So, it kind of turns the story upside down.

Is it the number of digits alone that tells us that, or some other
features as well?

Clack: Acanthostega had a number of primitive features. One of those was
the proportion of [the bones in] the forearm, of the radius to ulna to each
other. In most tetrapods, the ulna is longer than the radius, and that’s true
to almost all tetrapods, and most fossil ones as well. But in the fish, from
what tetrapods were supposed to evolve, it’s the other way round: the radius is
much longer than the ulna. And that was the condition in Acanthostega. It seemed to us
that the limb elements of Acanthostega
were showing us what the primitive condition was like for limbs in general. Also, the fact that the digits were variable in number through these early
tetratpods, suggested that the function of the digits in the limbs was quite
different from what we assumed. It’s a paddle basically.

You also discovered new features in Icthyostega…

Clack: We discovered that Icthyostega is a really enigmatic
animal. We’ve known this more or less since it was discovered, and the more we
found out about it, the weirder it looked. It’s got some features in which some
limbs elements, like the humerus, are more primitive than that of Acanthostega, and yet other aspects of
the anatomy of Icthyosthega suggest
it was more terrestrial than Acanthostega.
Acanthostega seems to be almost
certainly entirely aquatic, but Icthyostega
has a really robust front limb that looks as though it could at least raise
the front body off the ground, whereas the hind limb is a paddle and points
backwards towards the animal’s tail. We worked out how this animal could
move using information from synchroton CT scans of the limbs and
reconstruction software that can help you find out how the limbs actually
worked in 3D. It turns out that Icthyostega didn’t walk in a conventional manner. It looks as
though one of the possible modes that it used would be a source of crunching
motion, with the two front limbs together and the hind limbs acting as breaks
or supports, but not actually producing any power on land. They were used to
propel the animal in water, so for walking or for moving on land it used its
front limbs, sort of pulling it along. And in the water it used its hind limbs
as paddles for propulsion.

How did the first terrestrial animal walked?

Clack: We don’t really have enough
information to be sure about that, but people now have been using the same sort
of software and techniques to look at Acanthostega
in the same way. But being very much aquatic, it’s obviously not going to be
comparable in terms of what it was doing. The implication is that there were
lots of different experiments going on in locomotion and we have only looked at
the tip of the iceberg, in terms of the information that we’ve got, which is so
limited. For example, in 2011, scientists published some track ways that were found in
Poland that pre-date the Devonian tetrapods we had found by about 15 millions
years. We don’t know what made those track ways, but we know it was made by an
animal walking supported by water and using its limbs in an alternated fashion
[…]. So there were some animals around at this early stage that were using this
pattern of locomotion, but we don’t know what they looked like because we don’t
have any body fossils for them.

What does it take for a palaeontologist to take on an ambitious
expedition like your expedition to Greenland?

Clack: Again it was a series of lucky
breaks. The material from Greenland at the time belonged to the Danish
government. The material from Icthyostega,for example, was all in Copenhagen. I
got in touch with the then curator of the Geological Museum in Copenhagen and
told him about the material I had found in the Earth Sciences Department. And
the quality and amount of that material convinced him that there was a lot more
to be found. So he got in touch with the authorities in Denmark and the
Greenland Geological Survey (as it was called then) and they happened that year
to be setting up a 3-year project in the very area that we wanted to go. We
managed to jump on the bandwagon, their expedition, using their facilities and
transport arrangements, to get our expedition together. And the funding came to
a large extent from our museum in Cambridge, and a certain amount also from
Copenhagen and the Karlsberg Foundation. That’s how it was funded. We did try
the Research Council in the UK but they weren’t interested.

Have there been other findings throughout your career that got you
as excited as when you found Acanthostega?

Clack: Well actually, the project that
I’m working on now which is now half way through. The Tw:eed Project is a consortium looking at what happened at the end of the Devonian. As the
story goes… Devonian was the age of fishes, and at the end of the Devonian, quite
a lot of them got wiped out, there was a mass extinction. The cause of it isn’t
clear, but it seems to have been something climatic. The period after that, for
15 to 20 million years, was an almost complete blank in the fossil record,
certainly for tetrapods but also for almost everything else as well. [...] The problem was that after that period of 20 million years, when we begin
to pick up fossils of tetrapods again, they were extremely diverse. There was a huge variety of tetrapod forms, from
small ones the size of a mouse, to other ones that were three or four meters
long. So how did they get there? What happened after the end of the Devonian
that allowed them to do that? We knew nothing about how these things became
properly terrestrial. And it all happened in that gap. This
gap was first identified by an American palaeontologist called Al Romer, so
it’s called Romer’s gap. There were a few specimens from the period of this
gap known from Nova Scotia, although nothing formal had been published on
those. And I published a paper in the early 2000s on a complete specimen of a tetrapod from the middle of this gap that had been found in Dumbarton, in
Scotland. In subsequent years, some of my colleagues have been looking at the
appropriate sorts of sediments in the borders region in Northumberland, in
Scotland, for the rocks of this age. They found some material, and it’s that
material that we are beginning to work on, and we’re also finding a lot more.
We have found numerous fossils of tetrapods, several new sharks, new
lungfishes, all sorts of things. We’re beginning to get a handle on how
terrestrial features or adaptations in tetrapods could have arisen.

So it is possible to find fossils from the Romer’s gap...

Clack: Yes, that’s right. Our idea is
that this particular formation called the Ballagan Formation, which has been
known for many years and was described as the Scottish cement stone series, is
not commercially viable. There’s no coal and no decent limestone. In the 19th century
a lot of the carboniferous fossils were found by miners, and that’s how we knew
they were there. But because nobody has been looking for commercially viable
rocks, nobody has found anything, and because nobody has found anything, nobody
has looked. It’s a sort of self-fulfilling prophecy until you get somebody with
the determination to say, well they got to be there. And indeed, it turns out
that they were.

Do you think that a multidisciplinary approach is important for palaeontology, or is it just a trend?

Clack: This seems to be increasingly the
case, yes. […] In the 1970s and 1980s or earlier, palaeontologists tended to
work by themselves, just looking and describing the animals. They were doing
some fieldwork to find new stuff too, but definitely that was “one person,
one fossil” kind of thing. But now collaboration is the key word because
different people have different skills, and with all the new techniques that
are coming forward you need collaborations to get all those skills together.
And certainly I’ve collaborated with people from the Royal Veterinary College
for example, and people from the synchroton facility in Grenoble. You just
can’t work by yourself anymore, and this particular project was really perfect
for this kind of collaborative effort.

How has the development of modern instrumentation (isotope analysis,
computer modelling, X-ray computed tomography) changed the field?

Clack: Now we can think of asking and
answering questions that would have seemed impossible 10 or 15 years ago. We
can ask new questions about how things work, what that might mean,
and how the animals developed. And, of course, you’ve got geologists on one side,
and then you’ve got technicians, and people doing developmental biology on
modern creatures to look at how things could relate to what the fossil record
is finding. These collaborations are increasingly common. Developmental
biologists and Evo-Devo people are constantly coming to us and asking what we
see in the fossil record, and how could this fit with what they’re finding.
It’s really encouraging. […] Quite a few people are interested
in compiling large databases and then interrogating them; what fossils came from
this region, how many species are there in these various time slots and what
does the phylogeny tells us. That’s all very well but one fossil can overturn
any of that. You still need the data and that’s why it’s so encouraging also
that more people are going out and finding new stuff all the time, finding new localities and new areas of the world to explore. And at some of the
localities people thought were wiped out, they go back and find new
material there, so there’s a wealth of stuff. And of course, communication is so
much easier than it used to be.

What is the palaeontology of the future?

Clack: Oh, who knows? If you look at the
Society of Vertebrate Palaeontology website, they have their programme for their annual meeting which was in Berlin this year, and the diversity of talks is just stunning, where do we go from here?
Well, I think we still need to be fuelled by new material, but that new
material can overturn anything that I said! 50 years ago we thought we knew
everything about fossils and Palaeozoic vertebrates… no we don’t know, it has
been completely overturned since then and there’s no doubt it will be
overturned again in the next 50 years.

How can we change the way scientists are perceived by the
public?

Clack: The media like to portrait science
as rather esoteric, let's say. BBC tries to do a good job, but I think they have
very stereotyped ideas about science and they think the public can’t cope with
uncertainties. The message needs to get across that science is about questions and not about answers, and that’s hard to communicate.

What do you love the most about being a palaeontologist?

Clack: Solving the puzzle, interpreting
difficult material, and I think it’s probably one of the things I’m best at. I also quite enjoy writing the papers. I don’t find writing difficult, as I
know some people do.

What big exciting questions remain
out there for palaeontology, and which ones would you really like to see
answered?

Clack: In
terms of vertebrates, some of the big questions now are: what’s the origin of
vertebrates? How do we get limbs from fins? How do you get fins in the first
place? How do you get jaws and teeth, where are they coming form? That’s the
sort of thing we can relate to modern developmental genetics as well. Where we
can find links with other disciplines it’s really important. If
you look at the limb bones of the carboniferous animals, in many cases they’re
quite different from those of modern forms. How do we get terrestrially capable
limbs? Which bits have to be modified so that you can bear weight? What muscles
do you attach and how do they develop?

How would you explain to someone in
one sentence that it is important to fund and encourage more palaeontology
research?

Clack: It’s a bit like learning History,
you know what use is History? What use is the Arts? People don’t seem to ask
those questions, but what use is Palaeontology? Oh, that’s no use is it? Well
it’s a cultural exercise, it expands the mind, it tells us where we came from and it puts us in our place. It’s all part of the evolutionary story. It’s not
like a biomedical science where you want to help people, or invent some kid of
drug or something, it’s mind expanding blue skies, learning about the world.

What is the fossil of your dreams?

Clack: I
would like a sequence of strata with exceptionally well-preserved soft tissue
representations of Devonian forms so that we could find out what sort of
reproductive strategy they used. It’s what we call a Lagerstätten, like the Burgess Shale where we can
actually see soft tissue preservation of early tetrapods.

References:Pierce S.E. & John R. Hutchinson (2012). Three-dimensional limb joint mobility in the early tetrapod Ichthyostega, Nature, DOI: http://dx.doi.org/10.1038/nature11124Clack J.A. (2002). An early tetrapod from ‘Romer's Gap’, Nature, 418 (6893) 72-76. DOI: http://dx.doi.org/10.1038/nature00824Image credits: Museum of Zoology, University of Cambridge. Portrait, Chris Green, Department of Zoology, University of Cambridge.
An edited version of this interview was published in Lab Times in print on the 24-11-2014.